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• Minimac3 Cookbook : Pre-Phasing
  ...wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of the non-Pseudo-Autosomal Region (on ...an resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/downl
  4 KB (547 words) - 02:20, 30 January 2015
• Trial Enrichment
  This package contains source code and brief instruction of the method use in the paper by Hu et al, titled "T ...change all the number of random samples from 1e5 (100K) to 1e6 (1M) in the code
  2 KB (322 words) - 18:28, 21 May 2013
• RAREFY DOCUMENTATION
  ...likelihood-based method to prioritize individuals in family AND population samples. Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables.
  3 KB (455 words) - 05:08, 17 February 2015
• LibStatGen: VCF
  You will use both an <code>VcfFileReader</code> and an <code>VCfRecord</code> for reading VCF files. === <code>VcfFileReader</code> ===
  18 KB (2,634 words) - 16:09, 23 January 2013
• GotCloud: Creating a New Pipeline
  * Section names are specified between square brakets (<code>[]</code>) ...r a key defined in another section, use <code>$(otherSectionName/keyName)</code>
  10 KB (1,525 words) - 14:55, 31 August 2015
• VcfRefGen
  Source code can in: [[Media:vcfRefGen.0.1.4.tgz‎|VcfRefGen.0.1.4.tgz‎]] - Released |style=white-space:nowrap|<code>--in <filename></code>
  2 KB (332 words) - 15:53, 4 September 2014
• DosageConvertor
  ...ited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[# When <code>--type mach</code> is used, the <code>--format</code> parameter can only take values 1 or 2.
  8 KB (1,151 words) - 14:01, 18 January 2019
• QPLOT
  (1) Download the pre-compiled binary along with the source code as described in [[#Binary Download|Binary Download]]. ...[[#Source Code Distribution|Source Code Distribution]] on fetching source code and building instructions.
  16 KB (2,386 words) - 11:42, 2 February 2017
• RAREMETAL Change Log
  ** The source code has been optimized to prepare for incoming new meta-analysis method in next ** Fixed bug estimating kinshipX with female samples.
  8 KB (1,138 words) - 12:50, 14 March 2019
• Polymutt2
  *After downloading the source code, unzip and untar it, and cd polymutt2, and then type Make ...rated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
  4 KB (623 words) - 23:54, 10 November 2016
• Minimac3 - Full List of Options
  | File containing haplotype data for target (gwas) samples. Must be a VCF file. ...er estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]
  6 KB (941 words) - 19:34, 6 June 2016
• RAREMETALWORKER SPECIAL TOPICS
  ...make sure RAREMETALWORKER analyze chromosome X correctly, '''male must be code as 1 and female must be coded as 2''' in [[RAREMETALWORKER#PED_and_DAT_File * When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed
  3 KB (418 words) - 17:50, 16 March 2018
• FamLDCaller
  ...with that in .vcf file. The computation will be intensive if the number of samples are large.
  3 KB (435 words) - 10:05, 18 August 2014
• 1000 Genomes Project Pilot 1 SNP Calling
  key command: glfSplit<br>Source codes: ~goncalo/code/glfSplit/ == (5) Check total (aggregated over all individual samples) depth for each population, each platform ==
  7 KB (1,088 words) - 13:35, 10 March 2010
• Minimac4 - Full List of Options
  | File containing haplotype data for target (gwas) samples. Must be a VCF file. | This is number of samples to be stored in the memory before writing a VCF file piece
  8 KB (1,166 words) - 21:28, 1 December 2016
• ExomePicks
  A source code package can be downloaded from [http://csg.sph.umich.edu//abecasis/download The pedigree file describes relationships among individuals and indicates samples for whom DNA is available (and who can thus be selected for sequencing) and
  7 KB (964 words) - 10:01, 2 February 2017
• Biostatistics 830: Fall 2013 Edition
  The following is an extract from the School of Public Health's Student Code of Conduct [http://www.sph.umich.edu/academics/policies/conduct.html]: ...net.'' '''44''':955-9. PMID: 22820512 [[Biostatistics 830 - Code Snippets|[Code Snippets]]]
  8 KB (1,143 words) - 13:59, 2 September 2014
• Minimac3 ChangeLog
  immense help in making the code faster. -omosome X only male samples. Also added --rsid option to use
  10 KB (1,262 words) - 22:24, 6 June 2016
• Minimac4 Documentation
  ...ameter estimate; otherwise, a genetic map file for option <code>--mapFile</code> is required. ...is option is automatically ignored except when <code>--referenceEstimates</code> is OFF.
  8 KB (1,095 words) - 23:17, 19 July 2019
• Tutorial: Low Pass Sequence Analysis Answers
  ...the fifth nucleotide is encoded with the character "G". Its decimal ASCII code is 71, so the base quality of this nucleotide is 38 (71-33) [mpileup] 1 samples in 1 input files
  6 KB (849 words) - 04:10, 23 June 2016

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